


When Two became Three

by DarkHorseAsh



Category: Doctor Who, Doctor Who & Related Fandoms, Doctor Who (2005)
Genre: (but only for a chapter), (this really will be incredibly fluffy just give it a few chapters), Coming Out, Cuddling & Snuggling, Emotional Hurt/Comfort, Fluff, Hurt/Comfort, Implied/Referenced Self-Harm, Love, Panic Attacks, Polyamory, Polyamory Negotiations, Post-Episode: s07e05 The Angels Take Manhattan, Post-Traumatic Stress Disorder - PTSD, Sickfic, Touch-Starved
Language: English
Status: In-Progress
Published: 2018-01-14
Updated: 2018-03-02
Packaged: 2019-03-04 19:28:25
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 4,008
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/13371552
Author URL: https://archiveofourown.org/users/DarkHorseAsh/pseuds/DarkHorseAsh
Summary: Amy and Rory have been traveling with the doctor for so long, they can't imagine doing anything else.  But when they get stuck in New York, lost in time before they were born, what will it take to get them back to the Doctor?  And what will it take for them to realize how much they need him, too.





	1. Chapter 1

**Author's Note:**

> So, this first chapter actually has nothing to do with the angels take Manhattan, but I wanted background so, here it is. The next chapter starts right after we leave off at the end of that episode.

The Doctor woke up at midnight.  For a few moments, he wasn’t sure what it was that had woken him, until he felt the covers twisted around his limbs and the fact he was shaking violently.  He felt feverish, his brain foggy and afraid as he curled weakly into himself, letting out a moan of pain as his stomach cramped.  He considered going to get Amy or Rory, considered letting them help him, but the rest of his brain overrode that in a moment.  He was the last of the time lords, he was easily strong enough to cope with one little flu he didn’t need  _ help.   _ Except as his stomach gave another agonizing cramp, he couldn’t stop the tears from running down his cheeks as he wished for his friends.  He wanted to curl up with them, to let someone else take care of him for a change.  He imagined Amy kissing his head, Rory wrapped around him, a soft, lingering kiss.  The Doctor shook his head hard, moaning at the pain it caused as he forced his fantasies down.  He was their friend.  They were  _ engaged _ , getting married TOMORROW _.   _ He needed to get over it and get sleep so he could get better.

 

Rory wasn’t sure what had happened.  One moment he had been enjoying cuddling with his fiance, enjoying the bed in their room in the TARDIS now that the Doctor had, grudgingly, changed it into an actual bed.  The bunk beds had been...interesting, but after two nights Amy was tired of waking up on top of Rory and Rory was tired of waking up with Amy all but crushing him so they had gotten the Doctor to give them a real bed.  But somehow, in the span of five seconds, they’d gone from curled up together to jumping up as the TARDIS made an angry screaming noise.  Rory covered his ears, hissing in pain as Amy rushed to put her hands on the metal walls.  “What’s wrong, old girl?”  She crooned, running her hands over the metal soothingly as the TARDIS all but shook under her palms.  Rory ducked out of the room, still pulling on a shirt as he glanced around worriedly.  The TARDIS would often communicate with them in similar ways, sharp bursts of air or quiet noises when it thought something needed attention, but this was the most dramatic thing it had ever done and Rory was worried that meant something was really wrong.  

 

He kept walking, but the TARDIS kept putting him in the same hallway so he gave up on getting out and just opened the door he was nearest to.  It was dark, but there was slight light that showed he was clearly in some kind of bedroom.  Rory gave a soft ask to the TARDIS, and the room brightened slightly, so that he could see the room for real.  It was large, but messy, covered in bits of machinery and various nicknacks that looked like they came from a million different places in a million different times.  The floor was a fluffy black carpet, the ceiling painted with starts and circling letters that Rory could recognize as gallifreyan.  But what drew his attention was the bed in the back corner of the room.  It was round, and the Doctor was curled up in the middle of it under a blue blanket that was strikingly similar to the color of the TARDIS.

 

“Doctor?”  Rory questioned softly as he approached, noticing that the blanket was shivering slightly, as though the man underneath it was shaking.  The room was fully lit now, and Rory could see that the Doctor was shivering violently.  “Doctor.”  Rory spoke louder, becoming increasingly worried when the man didn’t respond.  He sat, resting one hand on the Doctor’s back and immediately becoming concerned because of the heat radiating through the thin fabric of the pajamas the time lord was wearing.  The Doctor twitched under his hand, shifting to blink up at him through glazed eyes.  “Rory.”  He mumbled gratefully, shifting to press his head against the nurse’s hand with a soft whine.  Rory softened as he gently asked “are you sick?”   
  


The Doctor nodded tiredly, feeling too bad to remind himself that he shouldn’t be cuddling up against Rory this desperately.  He knew humans from their time weren’t so great about platonic cuddling but he felt feverish and weak and exhausted and he just wanted someone to be there. “Mmm, yeah.  Flu.”  He mumbled, groaning tiredly.  Rory ran his long fingers through the man’s hair, which was plastered to his head with sweat, trying to figure out what to do with his friend.  He finally made a decision, moving and picking the timelord up, grunting slightly as he tried to find the best way to balance and not drop the sick man.  The Doctor shifted, groaning weakly in pain.  “I can walk.”  

 

Rory glared at him, not believing that for a moment, but he shifted to let the man stand, taking the moment of his hands being free to text Amy a quick message.  The Doctor managed two steps before his knees buckled and Rory caught him, tugging him back into his body as he gasped.  “Easy, breathe, Doctor.”  Rory soothed, slipping an arm around his waist to help him since he was almost positive there was no way the Doctor was going to let himself be carried.   Light-blue eyes met glazed green as the Doctor shifted to look at him more directly as they stumbled down the hallway, Rory taking the brunt of his weight.  “Where are we going”

 

“My and Amy’s room.”  Rory paused for a moment to look at the man.  “Hey, can Amy and I catch this?”  The Doctor shook his head, deciding against elaborating as his aching body sent another wave of pain into him.  He moaned, tightening his hands around Rory’s shoulders as Rory ran one hand soothingly over his back, walking more briskly.  “Easy, Doc.  Just a few more steps and we can get you in a warm bed again, hm?  Though I have to warn you, Amy is going to be all over taking care of you.  It’s a Thing she does whenever someone is sick.”  He was slightly worried by the Doctor’s lack of responding, the man half pressed against his side was so different from the emotional, enthusiastic, somewhat manic time lord he was used to.  

 

Amy was still up when Rory came in, sitting on the bed with a glass of water on the nightstand.  She hurried to the Doctor’s other side, so they all but carried him to the bed and got him tucked in, propped up on the pillows.  He groaned weakly, feeling too sick to try and jostle for his leadership position.  Rory all but forced the water into him, before pacing around the room slowly.  “Doctor, what exactly are the symptoms of the flu in time lords?”  The Doctor glanced over at him with a pained sigh.  “Fever, headache, stomach pain, nausea, vomiting, chills, muscle pain.”  He listed off automatically, before breaking off coughing painfully, curling into himself.  Amy moved to his side, eyes glancing worriedly up at Rory.  

 

“Are there any medications you can have?”  Rory questioned.  He knew most medication was a no go when it came to timelords, but he still wasn’t sure if that meant they had their own versions or not.  The Doctor groaned, shaking his head.  “Nothing for this except maybe painkillers.  In medbay.”  Amy moved towards the door, ducking outside to try and find the medbay as Rory considered what to do with their sick friend.  The Doctor was curled into himself, skin flushed with fever, shivering violently as he huddled under a blanket Amy had tucked around him.   He was the picture of misery, which caused Rory’s heart to break at the miserable look on the other man’s face. 

 

Rory moved to sit on the bed, resting one hand against the Doctor’s back.  He blinked in surprise as the sick man shifted to cuddle into his side, moaning weakly.  Amy slipped back into the room with a pill bottle, passing Rory two of the pills.  The nurse shifted to nudge the Doctor back into a sitting position, ignoring the weak glare he was getting as he passed them to him.  “Take these and then you can get some sleep.”  He promises the timelord, who obediently downed the pills before curling up back against Rory.  Rory glanced at Amy, who was pulling off her socks and climbing carefully over the Doctor to sit on his other side, resting one hand against his shoulder and closing her eyes.

 

The Doctor woke up the next morning groaning.  He barely made it to the bathroom before he was throwing up, gasping and shaking over the toilet.  Amy and Rory had heard him, following quickly to find him slumped on the tile floors, looking exhausted.  That time, he didn’t protest when Rory carried him back to the bed, tucking him back in after coaxing some more water into the sick man.  The Doctor was pale, long fingers wrapped around Amy’s hand as soon as he was back in the bed, seemingly unwilling to release the human at his side.  He whined plaintively as she moved, causing both to finally just settle in on either side till he was asleep again.

 

“Amelia, really, I’m fine!”  The Doctor protested weakly.  He had slept through pretty much the entire previous day, and was feeling a bit better.  However,  Amy still looked wildly unimpressed with the Time Lord, who still looked far too pale and sickly for her liking.  Rory had gone to reorganize the kitchen, as being cooped up in one room was stressing him out more than he would like to admit that it did.  The Doctor shrank under Amy’s ire, never able to stand up against the redhead as well as he usually could against people, so he just rolled to his other side and latched onto her shoulder again.  

 

It had been three days, and The Doctor was starting to realize why Rory had mentioned Amy’s becoming overbearing when someone was sick.  He was still barely being allowed out of bed, though he had to admit he could barely manage a dozen steps before wanting to fall over, but that was beyond the point!  He wasn’t a child! 

 

_ Except he couldn’t pretend he hated the way Amy would sit next to him and let him put his head in her lap, the ways her fingers would play with his hair.  He hadn’t had that much contact in years, since before he had murdered all of his kin, and he missed it more than he could bear. _

 

Rory slipped into the bedroom, having finished reorganizing the kitchen and every other room he went into on a regular basis.  He wished he could reorganize the workshop, but knew that the Doctor would probably have killed him, so he left it how it was.  Glancing towards the bed, he smiled slightly.  Amy was leaning against the headboard, head tipped forward to lean against her chest.  The Doctor lay with his head in her lap, one hand loosely gripping one of her hands as he slept.  Rory slipped out of his shoes and his sweater, climbing over the Doctor to lay on the other side of the man and let himself dream.

 

“Cmon, Ponds!”  Rory groaned, burying his head in his pillow.  He had  _ not  _ missed this, being woken up at obscure hours of morning because the Doctor wanted to go on another adventure.  But it was good to hear his friend feeling better, at least.  Amy was groaning on his other side, muttering “make him stop.”  With a sharp laugh, Rory sat up, nudging Amy awake with his elbow.  “Doubt that’s happening.  We should go see what he wants.”  Leaving his wife to get dressed, Rory ducked out into the consol room, grinning at the alien standing behind the controls.  “Rory the Roman!  I was thinking, we never did go to Rio.”  Rory couldn’t not smile at his friend’s enthusiasm, trying to shove the thoughts of how cute he looked standing there with his bowtie, brown jacket thrown over his shoulder, bouncing up and down in delight.  “Yeah, Doctor, that sounds good to me, too.”  


	2. Chapter 2

**Summary for the Chapter:**

> So, this chapter is based a little bit on the ideas of an awesome fic I read by blackcolumbia, who I really hope doesn't mind me borrowing the idea of using Bracewell. This is all angst, with very little comfort. I'd say it'll resolve soon, but the Doctor has more angst before he gets there. Enjoy!!!

No!”  The Doctor dropped to his knees, body shaking with the force of his grief as he knelt over the grave.  He pressed his hands into his eyes, not trying to stifle the tears running down his cheeks as he shook.  “Amy.  Rory.”  He whimpered, curling in on himself.  He could feel River behind him, watching the angels, keeping them away, but he couldn’t help but think that he wouldn’t mind if they got him.  He just didn’t  _ care  _ anymore, as he struggled to his feet and forced his way back to the TARDIS.

 

River had stayed for a few days, but then she was off, to do whatever it was River did when she wasn’t there watching them and he was left there, in that wooden box that had never felt more like a prison until that moment.  He all but tore her control panel apart in his rage, and the old ship just let him.  She missed their humans too, for she had always loved how they had taken care of her thief.  He had been happier than she had seen in years, since the Time War and everything it had brought.  

 

Amy and Rory were hardly better off.  Being stuck years before they were born was hard, but being separated from the Doctor, who they had scarcely been without for so long, well, that was  _ hell.   _ Rory got a job working as a Doctor, but Amy spent her days in silence, duly experiencing a world she had never wanted to be in.  

 

Neither of them were very good at this, at staying in one place.  Rory was forever taking long walks throughout the city, finding new things to do every spare moment so he wouldn’t sit long enough to have the memories overtake him.  The Doctor, bouncing up and down on his heels like an excited child, eyes glowing with excitement as they plunged towards whatever adventure would undoubtedly almost kill them.  Amy rolling her eyes as she cuffed the Alien around the head for whatever stupid thing he had done, warm fingers on his wrists on the beaches of Rio, laughing in the sand when the universe’s clumsiest alien managed to knock them all over into the waves, which turned into two hours of a water fight until, exhausted, they crawled out of the surf to collapse on the warm sand side by side, happy.  He didn’t want to remember but he couldn’t ever forget.

 

Amy was worse, spending most of her time reading or writing in their small apartment, losing herself in the memories that Rory fought so hard to ignore.  Warm bodies pressed on either side of her, soft kisses in damp hair, Rory’s hand wrapped around her hand as he reached up to kiss the Doctor, the look on the alien’s face, so old and so young all at once, the first time Rory gave him a hug when they didn’t die.

 

It had been a month since Manhattan.  The Doctor had considered going to London, to see Jenny and Vastra, but he had decided against it because he knew that they would ask about Amy and Rory and he couldn’t force himself to answer those questions.  So he had gone to the Vortex and stayed there.  He spent most of his time curled up on the bed they had shared, wrapped around one of the pillows in a desperate attempt to muffle his tears.  The TARDIS was getting increasingly worried about him, desperately trying to find a way back to New York but knowing that there was no way to.  She couldn’t destroy time. 

 

“We can’t go on like this!”  Rory cried, two months into living in New York.  “We  **can’t** .”  I mean, for the love of god, we saw dinosaurs on a space ship!   We’ve faced Daleks and not died!  I stood next to the damn pandorica for TWO THOUSAND YEARS!  We can find a way out of New York!”   Amy froze, turning to look at him with a look in her eyes that Rory knew all too well.  “Daleks.”  She breathed, and she sounded better, more alive, than she had in two months.  “That’s it.  That’s what we do.”

 

Amy was missing the TARDIS most at moments like this, clinging to a ship bouncing over the waves.  She had forgotten that travel in the 1900s was not nearly as good as when she had been growing up, and so she had spent most of the journey in their room, curled up, or being sick over the rail.  Rory, who did not seem to have this problem, had spent the time talking to people he found interesting or exploring the ship in case of a catastrophe.  It was something they both found themselves doing more and more.

 

They’d had to wait over two years, at this point, because Amy wasn’t sure she had the timing right and if it was too early they would never get another chance.  They had to be late enough.  They spent the first two year in New York and the second two in a London only Amy could recognize.  They spent four years hoping.  

 

“Hey there, metal boy.  Fancy seeing you here.  Remember me?”  The alleyway was dark, but it didn’t stop Edwin Bracewell from jumping like he had seen a ghost  step out of it to face him.  “Miss Pond!”  He breathed, looking delighted.  “How good to see you again.”  Amy smiled, too, even if it didn’t reach her eyes.  “It’s Mrs. Pond now, Edwin.  And I’ve got a favor to ask you.  Fancy building me something?”  


	3. Please

 

Rory often thought his wife was brilliant, when she was saving the world or forcing their alien to stop working himself to death, or when she was spending two years fighting her way onto a newspaper staff and reporting on things that they had only read about in history books.  But now, as he tugged himself from the wreckage of the transportation device that they couldn’t pronounce the name of, he was starting to wonder if she wasn’t nearly as insane as the Doctor.  

 

Amy was already out of the device and standing, practically vibrating in delight as she spun around to look at him, eyes shining in a kind of joy neither had felt since they had traveled to that cursed day in New York.  “Rory, look!”  He did, forcing his throbbing head up to study what was around him, immediately ignoring his discomfort as he realized where they were.  “Yes!” He cried in delight when he finally saw the scene before him.  “Yes yes yes!”  

 

The towers of New, times many, many times, New York stood out against the dark sky like stars, and Rory could have sobbed in relief because they were  _ there,  _ they had done it, they had gotten out of the 1900s and the world didn’t appear to be ending because of it.   Amy grinned, offering out her hand to Rory.  “Well, cmon, lets go figure out how to get to the spaceport!”  He couldn’t help but smile, infected by her overwhelming joy even as he ignored her hand and lagged a few steps behind her, feeling far more bruised than she looked but not caring anymore because _ they got out. _

 

It turned out they were a few miles from the main city.  It was dark, but neither was willing to wait till the next day even when logically they knew it wouldn’t really matter.  Amy was talking about something, explaining the city since Rory had only ever been there for a very short period of time, when they had been defeating giant slug creatures or something.  But it had a spaceport, and the technology to track people, and that was the only thing they really cared about. 

 

The TARDIS was growing increasingly concerned about her captain.  It had been over two months since he had left the vortex, except for a few very brief stops to refuel or to save a planet, but her timelord seemed to be more miserable than she had ever seen him, except in those first awful days after the end of the Time War.  

 

The Doctor was miserable.  He knew he had spent most of the last few months curled up on the bed, or pacing around the consol rooms in anger, but he couldn’t even find it in him to be angry at himself as he curled up in his old repair swing, face pressed into one of Rory’s old shirts.  He inhaled the scent, uncaring of the tears that ran down his face into the cloth and shook with the force of tears he would usually have refused to shed.  The TARDIS whined in his mind, mourning with him as she silently begged the universe to fix what it had broken even as she knew it wasn’t listening.   _ “He fixes you over and over!  Do something for  _ **_him_ ** _ for once _ .”  she snarled into the darkness of the universe as she closed her non-existent eyes and hoped. 

 

Amy and Rory weren’t fairing too well, either.  It had started pouring rain, leaving Rory struggling behind Amy, hissing in pain every few steps.  They’d only gotten maybe half-way there when Amy finally stopped and turned to look at him, softening at the pure misery written into her husband’s eyes as he shook like a drowned rat.  “Come on, there’s a house right there, we can stay there.”  She suggests, grabbing his arm and tugging him forward.  Rory grumbled under his breath but let himself be pulled.

 

The house was small, but to Amy it still looked very futuristic.  The outside was metal, but Amy managed to locate something that looked vaguely like a doorbell.  She pressed it, hoping that it wasn’t a trap of some kind as she was getting wetter by the moment and was desperately hoping to dry off.  It only took a moment before a young woman opened the door, looking at the shivering strangers on her doorstep in alarm.  

 

“Oh my goodness, come in.” she said quickly.  Amy made a noise of relief, all but dragging Rory inside as he struggled to keep his aching legs under him.  A moment later the walls made a sharp noise and began to all but blow dry them, leaving both bedraggled looking but far less soaking wet than they had a few moments before.  

 

Half an hour later, both were curled up in the small spare bedroom, Amy wrapped protectively around Rory, both dreaming of once again finding their madman’s blue box in the stars.  Amy shifted in her sleep, tucking Rory closer to her and wishing desperately for those cool arms to hold her like they had every night; even years in the 1900s had not weaned her and Rory of the only way they slept well being with him curled up around them.   _ Please come back to us.   _

  
The Doctor had finally left the vortex, after his ship had all but forced him to.  He ended up in a small planet rotating around a weird sun, but he couldn’t care less about that.  What he cared about was the fact he had apparently been here before, which he didn’t remember at all, and so the moment he walked into the town the royal guards had seized him.  He had none of his usual bravado, practically shaking from a lack of food and sleep and general unwellness, and so it had been easy for them to beat him and throw his unresisting body into a tiny cell.  He curled up around his own legs, soul screaming for relief as he silently begged them, too far gone to his misery to care how pathetic he sounded.   _ Please come back to me.  Please. _

**Author's Note:**

> I hope you enjoyed! if you had any ideas on what should be included in the future, let me know!


End file.
